More install notes on a Dell workstation:
So far everything is much easier. Desktop effects enabled and working by default. Must have an nvidia card.
commands:
sudo apt-get emacs
sudo apt-get emacs-snapshot
http://peadrop.com/blog/2007/01/06/pretty-emacs/








Ubuntu install notes:**
Hardware IBM/Lenovo Thinkpad T60p 2gb RAM

Read from the bottom up.
**
Brian Caffo July 2008

Had to reinstall for some strange reason:
Used gparted to break the root directory in two. This was the best decision ever. Now the old installation is there plus the new one.
Installed blubuntu
Installed gnome-do (note have to edit some config files to get it to search directories)
Installed gparted


ACK nothing is working on the random freeze problem. Here's my current solution. Undid all of the kernel options except pnpbios=off. Uninstalled the proprietary drivers for the video card. The sensors suggest that something is running at 73 Deg C, which is frigging hot. Trying to figure out what that is. I think it's the video card. I'm thinking that turning off the proprietary drivers will help this. I also turned on all of the services that had previously been off.

Also, I downloaded thinkfand
http://www.gambitchess.org/mediawiki/index.php/ThinkPad_Fan_Control
and cranked the gpu fan up to 100% always. It's still running at a steady 73+ degrees C.

EDIT: Hooray, I think that this did it! Turning on the ATI drivers cranked up the temp to 85 doing nothing. Uninstalled them again, rebooted and it's back to 71 degrees C. The fan control kicks ass.
EDIT: Turning ACPI back on fixed the shutdown problem.
EDIT: Also, I took away the pnpbios=off kernel option with no consequences (no boot errors).
EDIT: This appears to have done it.
EDIT: Turned off the ATI drivers. I think this alone may have just solved the problem.
EDIT: Everything works now, no freezes in a while.

Did this to try and fix the shutdown hangup problems. (from this link)

http://ubuntuforums.org/showthread.php?t=603054

Go to "System" -> "Administration" -> "Login Window". In the "General" tab, press "Edit Commands...", which will launch a window titled "Reboot, Halt, Suspend and Custom Command Preferences". In this window, select "Halt command" in the drop-down box for "Command Type:". Underneath it, in the "Path:" box, cut the verbiage in quotes: "Shut Down via gdm." After doing so, press "Apply Command Change", then paste the quoted phrase back into the "Path:" box and hit the "Apply Command Change" button again. Finally, go through the same process for the "Reboot command" in the "Command Type:" drop-down, again cutting the quoted phrase, applying the change, pasting the quote, and applying the change.

EDIT: This doesn't do anything.
EDIT: ignore this, see above

added pnpbios=off to the boot options (see below) because of the weird track pad problem
note I undid this. Turning it off in the grub menu stopped the error messages during boot.
Edit: I turned pnpboot off in the kernel options (for the version 19 kernel). Now the trackpad is back

EDIT: to try to fix the shutdown hangs I added apm_power_off=1 to /etc/modules
and apm=power_off to /boot/grub/menu.list
EDIT: This didn't work removed these edits
EDIT: tried deleting the -i in /etc/init.d/halt line:

halt -d -f $poweroff $hddown

EDIT: this didn't work (readded the i)
EDIT: added the kernel option acpi=force; this seems to have worked.
EDIT: no it didn't. I turned off several services and haven't had a problem since.
EDIT: ignore this, see above

Editing pdfs is sort of a pain in the ass. I installed jarnal to do this. Pdfedit doesn't work that well.
Also, I installed foxit reader under wine. To do this, I used the stand alone (portable) foxit reader app.
There's a linux version of foxit, but it didn't install for me.

Copy paste from emacs to external programs. This has always been a problem regardless of the OS.  Add these to .emacs file.

(setq x-select-enable-clipboard t)
(setq interprogram-paste-function 'x-cut-buffer-or-selection-value)

Worried still about random freezes. Added the noapic aipc=off nolapic kernel options:
https://help.ubuntu.com/community/GrubHowto
http://ubuntuforums.org/showthread.php?t=47330&page=4
Had to add these options to
/boot/grub/menu.list
# kopt=root=UUID=de537f1f-25da-4fc5-8522-50d54c697f7a ro noapic acpi=off nolapic

EDIT: This seems to have fixed it. Also all of the freezes have had something to do with Firefox 3. Maybe switch to FF2 also?
EDIT: ignore this, see above

Got the scanner to work: read:
http://ubuntuforums.org/showthread.php?t=667182
http://gkall.hobby.nl/gt6816-07b3-0412.html#download

From the second url, download the file cism216.fw
and put it in the location /usr/share/sane/gt68xx/cism216.fw
That was it, xsane worked out of the box then.

Getting the cell phone blue tooth dial up networking to work:
Phone's address **:**:**:**:**:** (actual address omitted)
Useful command line tools:

hcitool scan #scans for devices in discoverable mode
sudo hidd --connect      #connects to device
sdptool browse **:**:**:**:**:** ##browses the phone

note lsusb lists out all of the usb devices

The required chanel is 8 (for me)
edited /etc/bluetooth/rfcomm.conf
added /etc/chatscripts/verizon
/etc/ppp/peers/verizon

to test it: turn off wireless networking
to start it up, type:

pon verizon

to end type:

poff verizon

turn back on wireless networking

These web pages were helpful

https://help.ubuntu.com/community/BluetoothDialup
https://help.ubuntu.com/community/BluetoothSetup?highlight=(CategoryBluetooth)
https://help.ubuntu.com/community/BluetoothDialup/Verizon

created some start-up scripts in ~/bin

note to get FireFox working, you have to switch off "file -> offline mode"

EDIT: This web site
http://ubuntuforums.org/showthread.php?t=838891&highlight=1xevdo
totally nails how to do this via gnome-PPP. Make sure the device is connected and you hit "autoDetect"


Wrote some rsync backup shell scripts (have to be executed manually)
They're in ~/bin/pushTo*
pushToEnigma.sh uses ssh to sync everything in ~/toSync onto enigma
pushToDrive.sh uses ssh to sync everything in ~/. to the drive in the office.
There's some things that don't sync, look into this. (probably permissions).

The bluetooth errors were definitely drivers for the
built in BT thingy. A BT dongle worked fine out of the box. Still working
on using the cell phone's fast internet connections as a BT modem.
Edit - resolved, see above

Set up IMAP on thunderbird to back up gmail.
I found this page for setting up automatic downloads
http://kb.mozillazine.org/Checking_for_new_messages_in_other_folders_-_Thunderbird
Changed the about.config entry for
mail.check_all_imap_folders_for_new
to true
EDIT This doesn't seem to work. Followed the other advice on that page
EDIT This is more trouble than it's worth. Just am backing up gmail using POP

Running matlab using the nojvm option solved the printing
problem; even when the desktop effects are there.
So, you can save pngs etcetera as long as you don't start
the gui.

Still having random freezes (more when not docked)
Tried turning off powernowd (from the services) and
the bluetooth service. (Got these ideas from some web site).
Note - this seems to have worked; turned back on the BT services
Note - this is definitely a temperature problem created scripts in ~/bin to watch the temp; type "watch temp"
Note - see the temps by grep -i "thermal" /var/log/sys.log

xmedcon is in the ubuntu repository; it's super
easy to install.

Mricro was a little harder; you have to make sure
to download the right version then start it with
~/local/mricro/startmrico

There's some problems with 3d rendering in mricron

I also installed "dicom2"

To install spm5 in matlab I had to do the following:
1) Go into the src directory of spm5 and edit the makefile
   so that it ignores that uname -i gives "unknown". This
   amounted to commenting out a few lines and giving setting
   HARDAWARE=i386
2) do make and make install. It give warnings about the gcc version, but oh well

I couldn't get the shell mode to work in matlab emacs
it kept trying to bring up the desktop version. So I removed
all matlab commands in the path and created ones in ~/bin
so that the command "matlab" brings up the -nojvm -nosplash -nodesktop
version and "matlabGui" brings up the gui

Installed thinkfinger to get the fingerprint reader to work. The following command
was used
sudo tf-tool --acquire
the following output was given:
"Storing data (/home/bcaffo/.thinkfinger.bir)... done."
This verified
sudo tf-tool --verify
https://wiki.ubuntu.com/ThinkFinger

I had to install the libpam-thinkfinger library.
And run this command:

/usr/lib/pam-thinkfinger/pam-thinkfinger-enable

Now it works flawlessly. It only registers one finger, so as long as I don't lose it, I'm ok.

matlab desktop doesn't work when desktop effects are
turned on

Also note to turn on matlab, I didn't install
the license manager, it has to be run (it's
in ~/local/matlab/etc/)

Note: Same is true for rgl

Note this is a problem with Compiz fusion and opengl on ATI video cards

turning off desktop effects also stopped the
freezing up problem I had.
Edit - no it didn't
Edit - See comment above

http://start.ubuntu.com/8.10/Slow ssh loggins; the following cured it

Changed

GSSAPIAuthentication yes

to

GSSAPIAuthentication no

in /etc/ssh/ssh_config

Getting the vpn to use the library stuff was a pain in the ass
First, I downloaded the stuff off of the
JH web site (now in ~/local/vpn). I had
to install a kernel patch to get it to work.
Instructions are here:
http://www.blog.arun-prabha.com/2008/05/01/cisco-vpn-installation-issue-with-ubuntu-804-hardy-heron/

http://www.blog.arun-prabha.com/2006/11/16/installing-cisco-vpn-and-vpnc-in-ubuntu/

I had to use the patch command with "-p0" otherwise it did't work.

Created start script in ~/bin

note password pasting does work, it just doesn't look like it (doesn't fill in asterisks).

note2 vpnc looks much easier, just can't get the info to fill in.

Have to install emacs-snapshot to get a good looking emacs